The application of electrophoresis upon commercial threads is investigated for development of low-cost diagnostics assays, designed for the matrix separation and quantification of low abundance metabolites in complex samples - in this work riboflavin in human urine. Zone electrophoresis was evaluated upon 8 commercially available threads, with several synthetic threads exhibiting higher electroosmotic flow (EOF) and increased electrophoretic mobility of the rhodamine 6G, rhodamine B, and fluorescein. Of those tested, a nylon bundle was selected as the best platform, offering less band dispersion and higher resolution, a high relative EOF, whilst minimising the contribution of joule heating. A novel 3D printed platform was designed, based on a modular system, facilitating the electrophoresis process and rapid assembly, whilst offering the potential for multiplexed analysis or investigation of more complex systems. Using the thread-based electrophoresis system, riboflavin was determined in less than 2 min. The device exhibited a linear working range from 0.1 to 15 μg/mL of riboflavin in urine, and was in good agreement with capillary electrophoresis measurements.